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PINBOARD SUMMARY

Transposable Elements (TEs), first known as &#34;Jumping Genes&#34;, were discovered by Barbara McClintock in the 1950s and later on led to a Nobel Prize in 1983. Over the years, it has been widely recognized that TEs from different families constitute a considerable portion of most eukaryotic genomes, including over 50% in ours.

The Long Interspersed Element-1 (L1) is one of the most active human TEs and composes over 17% of the human genome. L1 transposition follows a ‘copy-and-paste’ mode, given that the “original copy” of L1 is kept in the genome after the event. The process includes the transcription of genomic L1 sequence, a reverse transcription of the RNA intermediate followed by the insertion of L1 cDNA into genomic locations with specific target sequences. Also the reverse transcriptase encoded by L1 can be hijacked by other TEs such as short interspersed elements (SINEs), while altogether different TE families are critical in shaping the modern human genome. Moreover, the regulatory impacts of TE activities have also been revealed in multiple cases such as transcription, RNA processing, and DNA methylation. Therefore, characterizing the transpositional activity of L1s and their interactions with the genomic landscape is critical for understanding genome evolution and function.

However, to date, the dynamics of L1 integration and fixation has not been studied comprehensively. And here for the first time, we investigate L1 transposition on the genome-wide scale and in the evolutionary framework, while considering interactions with an extensive range of genomic features. We also applied Interval-Wise Testing (IWT), a novel Functional Data Analysis tool, to contrast the genomic landscapes at multiple scales and identify signatures of L1 integration and fixation. This study sheds light on the dynamics of TE landscape and will advance our understanding of the structure, evolution and function of the human genome.